Alternatives and similar repositories for jvarkit

Users that are interested in jvarkit are comparing it to the libraries listed below

• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆424Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 11 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆471Updated last month
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆596Updated 2 weeks ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• pcingola / SnpEff
  ☆279Updated 4 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆419Updated 5 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆445Updated last week
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆509Updated this week
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 3 weeks ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆591Updated 6 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆722Updated last month
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆332Updated this week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆271Updated 5 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆502Updated 7 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆510Updated 3 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆372Updated 3 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated 3 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆242Updated 2 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆377Updated last year
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆242Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆511Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆329Updated 3 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆340Updated last month